Ilans final edits

[igronau]

I'm just pushing my latest edits now. Will follow up with a more detailed description of what I did and the final minor tasks left. Stay tuned...

[igronau]

Summary of main changes: (highlighted in bold are some action items)

1. A few minor additions to abstract. I'd like others to review the new abstract to make sure it conveys the main points we wish to make in the paper
2. Intro: last paragraph was edited to provide a more comprehensive review of the paper, while still focusing on the "guidelines" section
3. The utility of stdpopsim section: this section was a bit scattered, with rough transitions between paragraphs. I made some minor adjustments to improve the flow between the three paragraphs and focus on the main ideas.
4. Slight graphical modifications of fig 1 (thanks, @lauterbur ).
5. The paragraph on gene conversion in the "additions to stdpopsim" was completely rewritten to describe the new way we parameterize GC. @petrelharp and Franz should review this to make sure I got everything correct. There are also some potential updates to the EscCol model that may require some additional tweaks here. See my comments to this PR.
6. Added references for various issues having to do with mis-specification of the demographic model (in the "Basic setup" subsection). I tried, but couldn't find additional references for the main point that mis-specifying the demographic model may lead to unrealistic patterns of variation. We're currently using Navascues and Emerson (2009), but @petrelharp rightfully suggested that there likely are other/better references. Do any good references come to mind?
7. In the "missing pieces" subsection, I edited table 1 to try to clarify the last column. Not sure how good it is. This definitely deserves a good review. Following @lauterbur's edits, we now don't mention any of this in the main text and it's only described in the table. I think it works nicely, as long as we get the table to be 100% clear. I also followed @jeromekelleher's suggestions and streamlined the 2nd and 3rd paragraphs in that subsection to drive the main message.
8. The AnoGam example. @lauterbur is creating a figure to add here based on what we have in the docs. I also made some edits to emphasize the lessons we can learn from this example. I recall people suggesting that there is more we can mention here about the QC, but I couldn't find anything worth mentioning from the QC issues. If you remember anything specific, let me know (@andrewkern? @petrelharp?).
9. I didn't yet make a thorough pass over the conclusions, but they look quite good in the current state, so I don't think I'll make any significant changes there.
10. Added a short acknowledgement statement to workshop participants. Please review this. We also need to make sure that all funding is mentioned in the last section.

[petrelharp]

adding_species_manuscript-diffmain.pdf Here's a latexdiff of the changes. For the record, to do this I did:

git checkout main
git pull origin
git fetch origin pull/68/head:ilan_pr
git checkout ilan_pr
latexdiff-git -r main adding_species_manuscript.tex
pdflatex adding_species_manuscript.tex
bibtex adding_species_manuscript.aux
pdflatex adding_species_manuscript.tex
pdflatex adding_species_manuscript.tex

[petrelharp]

Generally, looks great! I've made comments in a few places. Thanks a bunch!

[igronau]

I pushed a version which addresses @petrelharp's comments regarding the text on gene conversion. I now call it non-crossover recombination throughout the manuscript, unless we explicitly refer to gene conversion (in eukaryotes). I'll continue with other comments and edits later.

[igronau]

Pushed some more edits incorporating comments from @petrelharp , @jeromekelleher , @lauterbur. LatexDiff attached: adding_species_manuscript-diff.pdf

[igronau]

This latest commit contains some additional edits to the paragraph on partial genome builds in the "missing pieces" section, following discussion with @petrelharp. Let me know if you have any more comments or suggestions regarding this delicate issue